A Bayesian method for pulsar template generation

Extracting Times of Arrival from pulsar radio signals depends on the knowledge of the pulsars pulse profile and how this template is generated. We examine pulsar template generation with Bayesian methods. We will contrast the classical generation mechanism of averaging intensity profiles with a new approach based on Bayesian inference. We introduce the Bayesian measurement model imposed and derive the algorithm to reconstruct a "statistical template" out of noisy data. The properties of these "statistical templates" are analysed with simulated and real measurement data from PSR B1133+16. We explain how to put this new form of template to use in analysing secondary parameters of interest and give various examples: We implement a nonlinear filter for determining ToAs of pulsars. Applying this method to data from PSR J1713+0747 we derive ToAs self consistently, meaning all epochs were timed and we used the same epochs for template generation. While the average template contains fluctuations and noise as unavoidable artifacts, we find that the "statistical template" derived by Bayesian inference quantifies fluctuations and remaining uncertainty. This is why the algorithm suggested turns out to reconstruct templates of statistical significance from ten to fifty single pulses. A moving data window of fifty pulses, taking out one single pulse at the beginning and adding one at the end of the window unravels the characteristics of the methods to be compared. It shows that the change induced in the classical reconstruction is dominated by random fluctuations for the average template, while statistically significant changes drive the dynamics of the proposed method's reconstruction. The analysis of phase shifts with simulated data reveals that the proposed nonlinear algorithm is able to reconstruct correct phase information along with an acceptable estimation of the remaining uncertainty.Comment: 21 pages, 16 figures, submitted to MNRA

Language, Motor, and Cognitive Outcomes of Toddlers Who Were Born Preterm

Purpose: The purpose of this study was to examine the language, motor, and cognitive abilities of children born preterm in four categories: (a) healthy preterm infants, (b) infants of diabetic mothers, (c) infants with respiratory distress syndrome, and (d) infants with chronic lung disease when the children were 30 months, uncorrected age. Comorbidity of language, motor, and cognitive skills was examined, along with predictor variables. Method: A total of 148 children who were born preterm participated and were assessed using bivariate tests and logistic regression on standardized assessment scores. Results: Controlling for the children’s gestational age (GA), overall language ability was significantly lower in the infants of diabetic mothers group compared to the healthy preterm infant group, and expressive language skills were significantly lower for the chronic lung disease group than the respiratory distress syndrome group. The children with language delays on at least one measure were significantly more likely to have cognitive, motor, or both delays. Lower maternal education was a significant predictor for language and cognitive delays, and younger GA was a significant predictor for language, motor, and cognitive delays. Conclusion: Assessment of the preterm infant from a biosystems approach allows the speech-language pathologist to take into consideration maternal education, diagnosis at preterm birth, and GA, which were found to impact the language, motor, and cognitive outcomes of children born preterm. Our findings further reinforce the concept of the whole child in that children born preterm who display language delays should be screened for co-occurring motor and/or cognitive delays

An improved SPH scheme for cosmological simulations

We present an implementation of smoothed particle hydrodynamics (SPH) with improved accuracy for simulations of galaxies and the large-scale structure. In particular, we combine, implement, modify and test a vast majority of SPH improvement techniques in the latest instalment of the GADGET code. We use the Wendland kernel functions, a particle wake-up time-step limiting mechanism and a time-dependent scheme for artificial viscosity, which includes a high-order gradient computation and shear flow limiter. Additionally, we include a novel prescription for time-dependent artificial conduction, which corrects for gravitationally induced pressure gradients and largely improves the SPH performance in capturing the development of gas-dynamical instabilities. We extensively test our new implementation in a wide range of hydrodynamical standard tests including weak and strong shocks as well as shear flows, turbulent spectra, gas mixing, hydrostatic equilibria and self-gravitating gas clouds. We jointly employ all modifications; however, when necessary we study the performance of individual code modules. We approximate hydrodynamical states more accurately and with significantly less noise than standard SPH. Furthermore, the new implementation promotes the mixing of entropy between different fluid phases, also within cosmological simulations. Finally, we study the performance of the hydrodynamical solver in the context of radiative galaxy formation and non-radiative galaxy cluster formation. We find galactic disks to be colder, thinner and more extended and our results on galaxy clusters show entropy cores instead of steadily declining entropy profiles. In summary, we demonstrate that our improved SPH implementation overcomes most of the undesirable limitations of standard SPH, thus becoming the core of an efficient code for large cosmological simulations.Comment: 21 figures, 2 tables, accepted to MNRA

Effect of wearing a face mask on hand-to-face contact by children in a simulated school environment: the Back-to-School COVID-19 Simulation Randomized Clinical Trial

Importance Wearing a face mask in school can reduce SARS-CoV-2 transmission but it may also lead to increased hand-to-face contact, which in turn could increase infection risk through self-inoculation. Objective To evaluate the effect of wearing a face mask on hand-to-face contact by children while at school. Design, Setting, and Participants This prospective randomized clinical trial randomized students from junior kindergarten to grade 12 at 2 schools in Toronto, Ontario, Canada, during August 2020 in a 1:1 ratio to either a mask or control class during a 2-day school simulation. Classes were video recorded from 4 angles to accurately capture outcomes. Interventions Participants in the mask arm were instructed to bring their own mask and wear it at all times. Students assigned to control classes were not required to mask at any time (grade 4 and lower) or in the classroom where physical distancing could be maintained (grade 5 and up). Main Outcomes and Measures The primary outcome was the number of hand-to-face contacts per student per hour on day 2 of the simulation. Secondary outcomes included hand-to-mucosa contacts and hand-to-nonmucosa contacts. A mixed Poisson regression model was used to derive rate ratios (RRs), adjusted for age and sex with a random intercept for class with bootstrapped 95% CIs. Results A total of 174 students underwent randomization and 171 students (mask group, 50.6% male; control group, 52.4% male) attended school on day 2. The rate of hand-to-face contacts did not differ significantly between the mask and the control groups (88.2 vs 88.7 events per student per hour; RR, 1.00; 95% CI, 0.78-1.28; P = >.99). When compared with the control group, the rate of hand-to-mucosa contacts was significantly lower in the mask group (RR, 0.12; 95% CI, 0.07-0.21), while the rate of hand-to-nonmucosa contacts was higher (RR, 1.40; 95% CI, 1.08-1.82). Conclusions and Relevance In this clinical trial of simulated school attendance, hand-to-face contacts did not differ among students required to wear face masks vs students not required to wear face masks; however, hand-to-mucosa contracts were lower in the face mask group. This suggests that mask wearing is unlikely to increase infection risk through self-inoculation. Trial Registration ClinicalTrials.gov Identifier: NCT0453125

A Deficiency of Ceramide Biosynthesis Causes Cerebellar Purkinje Cell Neurodegeneration and Lipofuscin Accumulation

Sphingolipids, lipids with a common sphingoid base (also termed long chain base) backbone, play essential cellular structural and signaling functions. Alterations of sphingolipid levels have been implicated in many diseases, including neurodegenerative disorders. However, it remains largely unclear whether sphingolipid changes in these diseases are pathological events or homeostatic responses. Furthermore, how changes in sphingolipid homeostasis shape the progression of aging and neurodegeneration remains to be clarified. We identified two mouse strains, flincher (fln) and toppler (to), with spontaneous recessive mutations that cause cerebellar ataxia and Purkinje cell degeneration. Positional cloning demonstrated that these mutations reside in the Lass1 gene. Lass1 encodes (dihydro)ceramide synthase 1 (CerS1), which is highly expressed in neurons. Both fln and to mutations caused complete loss of CerS1 catalytic activity, which resulted in a reduction in sphingolipid biosynthesis in the brain and dramatic changes in steady-state levels of sphingolipids and sphingoid bases. In addition to Purkinje cell death, deficiency of CerS1 function also induced accumulation of lipofuscin with ubiquitylated proteins in many brain regions. Our results demonstrate clearly that ceramide biosynthesis deficiency can cause neurodegeneration and suggest a novel mechanism of lipofuscin formation, a common phenomenon that occurs during normal aging and in some neurodegenerative diseases

Ceramides and mitochondrial fatty acid oxidation in obesity

Obesity is an epidemic, complex disease that is characterized by increased glucose, lipids, and low-grade inflammation in the circulation, among other factors. It creates the perfect scenario for the production of ceramide, the building block of the sphingolipid family of lipids, which is involved in metabolic disorders such as obesity, diabetes, and cardiovascular disease. In addition, obesity causes a decrease in fatty acid oxidation (FAO), which contributes to lipid accumulation within the cells, conferringmore susceptibility to cell dysfunction. C16:0 ceramide, a specific ceramide species, has been identified recently as the principal mediator of obesity-derived insulin resistance, impaired fatty acid oxidation, and hepatic steatosis. In this review, we have sought to cover the importance of the ceramide species and their metabolism, the main ceramide signaling pathways in obesity, and the link between C16:0 ceramide, FAO, and obesity.This work was supported by the Ministry of Spain (MINECO) Grants SAF2013-45887-R (to L.H.), SAF2014-52223-C2-1-R (to D.S.), and SAF2014-52223-C2-2-R (to N.C.), and cofunded by the Fondos Europeos de Desarrollo Regional (FEDER); and by Centro de Investigacion Biom ´ edica en Red de Fisiopatolog ´ ´ıa de la Obesidad y la Nutricion (CIBEROBN) Grant CB06/03/0001 ´ (to D.S.); Government of Catalonia Grant 2014SGR465 (to D.S.); Marato TV3 Foundation (to D.S., N.C.); and the ´ European Foundation for the Study of Diabetes (EFSD)/ Janssen-Rising Star and L’Or´eal-UNESCO “For Women in Science” research fellowships (to L.H.)Peer reviewe

Rambrain - a library for virtually extending physical memory

We introduce Rambrain, a user space C++ library that manages memory consumption of data-intense applications. Using Rambrain, one can overcommit memory beyond the size of physical memory present in the system. While there exist other more advanced techniques to solve this problem, Rambrain focuses on saving development time by providing a fast, general and easy-to-use solution. Rambrain takes care of temporarily swapping out data to disk and can handle multiples of the physical memory size present. Rambrain is thread-safe, OpenMP and MPI compatible and supports asynchronous I/O. The library is designed to require minimal changes to existing programs and pose only a small overhead. Keywords: Memory management, Physical memory limitations, Abstraction library, System paging, Open source, MPI/OpenM

Using Computer Programs for Language Sample Analysis

Purpose: Although language sample analysis is widely recommended for assessing children's expressive language, few school-based speech-language pathologists routinely use it, citing a lack of time, resources, and training (pavelko, owens, ireland, & hahs-vaughn, 2016). The purpose of this clinical tutorial is (a) to describe options for language sample analysis using computer programs and (b) to demonstrate a process of using language sample analysis focused on the assessment of 2 preschool children as case studies. Method: We provide an overview of collecting and analyzing child language samples and describe 3 programs for language sample analysis: 2 dedicated software programs (computerized language analysis [macwhinney, 2000] and systematic analysis of language transcripts [miller & iglesias, 2015]) and 1 protocol for using word processing software to analyze language samples (sampling utterances and grammatical analysis revised; pavelko & owens, 2017). We also present analysis results from each program for play-based language samples from 2 preschool children and detailed analysis of the samples with potential treatment goals. Results: Each program offers different analyses, comparison databases, and sampling contexts. We present options for additional analysis, clinical interpretations, and potential treatment goals based on the 2 preschool cases. Conclusion: Clinicians can use computer programs for language sample analysis as part of a process to make naturalistic language assessment more feasible